# HG changeset patch
# User bgruening
# Date 1486987828 18000
# Node ID b4cd69acd431234506a6a6b872c3fa4e490bf2a2
# Parent  e51dba707cf1df5fe6dff934a65891318c2a05eb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit bff5ba839e2cb63792b0d25018460d76eb398002

diff -r e51dba707cf1 -r b4cd69acd431 PileOMeth.xml
--- a/PileOMeth.xml	Sat Dec 10 18:07:50 2016 -0500
+++ b/PileOMeth.xml	Mon Feb 13 07:10:28 2017 -0500
@@ -37,6 +37,9 @@
                 #if str($main_task.CTOB).strip() != "":
                     --CTOB $main_task.CTOB
                 #end if
+                $main_task.keepSingleton
+                $main_task.keepDiscordant
+                $main_task.fraction
             #end if
 
             #if $advanced_options.options=="yes":
@@ -60,6 +63,8 @@
             $input_sortedAlignBAM
 
             #if $main_task.task == "mbias":
+                $main_task.keepSingleton_mbias
+                $main_task.keepDiscordant_mbias
                 out_mbias &&
                 touch out_mbias_OT.svg &&
                 touch out_mbias_OB.svg &&
@@ -108,8 +113,15 @@
                 <param name="OB" type="text" value="" label="Original bottom strand bounds (comma-separated, no spaces)" />
                 <param name="CTOT" type="text" value="" label="Complementary to the original bottom strand bounds (comma-separated, no spaces)" />
                 <param name="CTOB" type="text" value="" label="Complementary to the original bottom strand bounds (comma-separated, no spaces)" />
+                <param name="keepSingleton" type="boolean" checked="false" truevalue="--keepSingleton" falsevalue="" />
+                <param name="keepDiscordant" type="boolean" checked="false" truevalue="--keepDiscordant" falsevalue="" />
+                <param name="fraction" type="boolean" checked="false" truevalue="--fraction" falsevalue="" />
+                
             </when>
-            <when value="mbias"/>
+            <when value="mbias">
+                <param name="keepSingleton_mbias" type="boolean" checked="false" truevalue="--keepSingleton" falsevalue="" />
+                <param name="keepDiscordant_mbias" type="boolean" checked="false" truevalue="--keepDiscordant" falsevalue="" />
+            </when>
         </conditional>
         <conditional name="advanced_options">
             <param name="options" type="select" label="Advanced options">